-C  ConfigFile		    
             A configuration file to be separately provided. Mandatory parameter. 
             Current package includes a sample configuration file named "configfile". 
             Details of the entries in this file are mentioned later.
              
-f  FASTQ1          
            Read 1 (or forward strand) of paired-end sequencing data  [.fq|.gz|.bz2]. 
			Or, even an aligned genome (.bam file) can be provided.
        
-r  FASTQ2          
            R2 of pair-end sequencing data [.fq|.gz|.bz2]. If not provided, and the -f parameter 
            is not a BAM file, the input is assumed to be single ended.

-n  PREFIX           
            Prefix string of output files. For example, -n "TEST" means that the 
            output filenames start with the string "TEST".

-g  BOWTIE2_GENOME   
            Bowtie2 indexed reference genome. Basically, the folder containing 
            the bwt2 indices are to be provided. 
            Mandatory parameter if user provides fastq files as input (-f and -r options).
			If user provides .bam files as input (-f option) then no need to provide this value.

-d  OutDir 			  
            Output directory which will contain all the results.

-c  CONTROLBAM		 
         	Control file(s) used for peak calling using MACS2. One or more 
			alignment files can be provided to be used 
			as a control. It may not be specified at all, in which 
			case MACS2 operates without any control. 
			Control file can be either in BAM or in  (tagalign.gz) format. 
			If multiple control files are provided, user needs to ensure that all of the 
			control files follow the same format (i.e. either all BAM or all TAGAlign).
			Example: -c control1.bam -c control2.bam puts two control files for using in MACS2.
	
			Conversion from BAM to TagAlign.gz format can be done using the script "TagAlign.sh" 
			provided within the folder "bin".
	
-w 	BigWigGenome	 
			Reference genome which is used to convert BAM file to a BigWig file. 
			Used for visualization track creation purpose. 
			If -g option is enabled (i.e. the Bowtie2 index genome is provided) 
			then this option is not required. 
			Otherwise, this is a mandatory parameter. Allowed values are 'hg19' 
			(default), 'mm9', 'hg38', and 'mm10'.		
	
-D  DEBUG_TXT		 
			Binary variable. If 1 (recommended), different statistics corresponding to 
			quality metrics and reads are printed. Useful when a summary of a large set 
			of ATAC-seq samples are to be generated.
	
-q  MAPQ_THR		 
			Quality value threshold, below which the mapped reads are removed (Default 30).
	
-p  PEAKCALLGENOMESIZE 
			genome size parameter for MACS2 peak calling ("hs", "mm", "ce", "dm": default "hs")

-O 	Overwrite		 
			Binary variable. If 1, overwrites the existing files (if any). Default = 0.
					 
-t  NUMTHREADS              
			Number of sorting, Bowtie2 mapping THREADS [Default = 1]. For parallel processing of Bowtie2, 
			user should specify > 1 value such as 4 ot 8.
	
-m  MAX_MEM          
			Set max memory used for PICARD duplication removal [Default = 8G].
	
-a  ALIGNVALIDMAX	 
			Set the number of (max) valid alignments which will be searched [Default = 4] 
			for Bowtie2.
	
-l  MAXFRAGLEN 		 
			Set the maximum fragment length to be used for Bowtie2 alignment [Default = 2000]

picardexec=
	Path of Picard tool executable
	Example: /home/sourya/packages/picard-tools/picard-tools-2.7.1/picard.jar

HOMERPath=
	Path of HOMER (after installation)
	Example: /home/sourya/packages/HOMER/bin/

DeepToolsDir=
	Path of deepTools executable
	Example: /home/sourya/packages/deepTools/deepTools2.0/bin/

RPackageExec=
	Installed R package directory.
	Example: /home/sourya/R-3.4.3/bin/Rscript
	If left as blank, default Rscript installed in the system will be invoked.

NarrowPeakASFile=
	file (SQL) required to convert the narrowPeak file to the bigBed format
	Download the file from this link (and save):
	https://genome-source.gi.ucsc.edu/gitlist/kent.git/blob/master/src/hg/lib/encode/narrowPeak.as
	Specify the location of this downloaded file:
	Example: /home/sourya/genomes/chrsize/narrowPeak.as

BigNarrowPeakASFile=
	file (SQL) required to convert the bignarrowPeak file to the bigBed format
	Download the file from this link (and save):
	https://genome.ucsc.edu/goldenPath/help/examples/bigNarrowPeak.as
	Specify the location of this downloaded file:
	Example: /home/sourya/genomes/chrsize/bigNarrowPeak.as
	
BroadPeakASFile=
	file (SQL) required to convert the broadPeak file to the bigBed format
	Download the file from this link (and save):
	https://genome-source.gi.ucsc.edu/gitlist/kent.git/blob/master/src/hg/lib/encode/broadPeak.as
	Specify the location of this downloaded file:
	Example: /home/sourya/genomes/chrsize/broadPeak.as
	
RefChrSizeFile=
	files containing chromosome size information
	two column file storing the size of individual chromosomes
	Downloaded from the link (depends on the reference Chromosome employed):
	For example, the hg38.chrom.sizes file for the hg38 database is located at 
	http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.chrom.sizes.
	Alternatively, Use the "fetchChromSizes" script from the UCSC repository 
	to get the appropriate chromosome size file.
	Specify the location of this downloaded file:
	Example: /home/sourya/genomes/chrsize/hg38.chrom.sizes
	
RefChrFastaFile=
	Fasta file of the reference Chromosome.
	Can be downloaded from the link:
	http://hgdownload.cse.ucsc.edu/downloads.html
	Example: /home/sourya/genomes/Complete_Genome/hg38/hg38.fa
	
RefChrAnnotFile=
	file containing reference UCSC annotation (.gtf format) 
	corresponding to the reference Chromosome.
	Can be downloaded from the link:
	http://hgdownload.cse.ucsc.edu/downloads.html
	Example: /home/sourya/genomes/Annotation/hg38/UCSC/hg38_UCSC_Annotation.gtf

F1: Alignment_MAPQ${MAPQ_THR}

	f0: Bowtie2_Init_Align.sam
		Initial alignment by Bowtie2 (if fastq files are provided as the input.)
	f1: UniqMappedRead.bam
		Initial alignment after unique mapping.
	f2: Bowtie2_del_Random.bam
		Alignment after deleting random reads.
	f3: Bowtie2_del_Mitch.bam: 
		After deleting mitochondrial reads.	
	f4: ${PREFIX}.align.sort.MAPQ${MAPQ_THR}.bam
		Sorted, and MAPQ thresholded alignment.
	f5: ${PREFIX}.align.sort.MAPQ${MAPQ_THR}.bam.bai
		Corresponding index.
	f6: ${PREFIX}.align.sort.MAPQ${MAPQ_THR}.rmdup.bam
		De-duplicated alignment (used for subsequent operations)
	f7: ${PREFIX}.align.sort.MAPQ${MAPQ_THR}.picard_metrics.txt
		Corresponding PICARD metrics log file.

	F1: ATAC_Seq_QC_New:

		This folder contains ATAC-seq QC metrics and summary statistics
		when computed by the package ATACseqQC. If the input data is single end, 
		only a file "Summary_QC.txt" is generated, containing the current 
		sequence specific summary metrics. For paired end input data, 
		the package also shows the library complexity, fragment size 
		distribution, nucleosome positioning, footprint analysis, and 
		motif entrichment. For details, please check the reference 
		manual of ATACseqQC in 
		https://bioconductor.org/packages/release/bioc/vignettes/ATACseqQC/inst/doc/ATACseqQC.html
		
F2: Out_BigWig
	f1: ${PREFIX}.bw 
		bigwig file for track visualization.

F3: Out_BigWig_NormCov:
	f1: ${PREFIX}_NormCov.bw
		bigwig file for track visualization (after normalizing the coverage).

F4: MACS2_Default_*
	Contains peaks employing MACS2 with default parameters.
		f1: *.narrowPeak: narowpeak formatted output with P-value threshold of 0.01
		f2: *.narrowPeak_Q0.05filt: peaks with Q-value threshold of 0.05
		f3: *.narrowPeak_Q0.01filt: peaks with Q-value threshold of 0.01
		f4: *.broadPeak: broadpeak formatted output with P-value threshold of 0.01
		f5: *.broadPeak_Q0.05filt: peaks with Q-value threshold of 0.05
		f6: *.broadPeak_Q0.01filt: peaks with Q-value threshold of 0.01
		f7: out_FRiP.txt: FRIP statistics for the narrow and broad peaks.
		f8: Peak_Statistics.txt: number of peaks
		F9: Peak_Annotate_Q*:
			For Q-value thresholds of either 0.01 or 0.05, contains the 
			HOMER based annotations.
		
		In addition, files *.bb denote corresponding big-bd formatted peaks,
		useful for USCSC track visualization.
		
F5: MACS2_Ext_*
	Contains peaks employing MACS2 with the parameters:
		--nomodel --nolambda --shift 0 --extsize 200
	File structure is similar as above.
	
f8: out_NRF_MAPQ${MAPQ_THR}.txt
	Metric NRF
	
f9: Read_Count_Stat.txt
	Read count statistics.

Rscript ResSummary.r [positional_arguments]:

1) OutBaseDir: 
	Directory under which results of all the different samples are stored 
	(like /home/sourya/Results as mentioned above)

2) OutFile: 
	Output file which will store the summarized results. 
	Default: Results_All_Samples_Summary.xls.

1) IDRMain.sh

2) IDR_SubSampleBAM_Main.sh

The first script, IDRMain.sh, performs IDR between two or more 
input peak files (we have used peaks estimated from MACS2). The parameters 
corresponding to this script are as follows:

-I  InpFile        	 
		A list of input peak files (obtained from MACS2 - in .narrowPeak or .narrowPeak.gz format). 
		At least two peak files are required. 

-P 	PathIDRCode		 
		Path of the IDRCode package (Kundaje et. al. after its installation). 
		Please check the "Required packages" section for the details.

-d  OutDir 		 	 
		Output directory (absolute path preferred) which will store the IDR results.

-n 	PREFIX 			 
		Prefix of output files. Default 'IDR_ATAC'.

A sample execution of this script is as follows:

./IDRMain.sh -I peak1.narrowPeak -I peak2.narrowPeak -I peak3.narrowPeak -P /home/sourya/packages/idrCode/ -d /home/sourya/OutDir_IDR -n 'IDR_test'



The second script, IDR_SubSampleBAM_Main.sh, takes input of two or more BAM files, 
estimates peaks from these BAM files, and then performs IDR analysis. The parameters 
corresponding to this script are as follows:

-I  InpFile        	 
		A list of input BAM files. At least two BAM files are required. 

-P 	PathIDRCode		 
		Path of the IDRCode package (Kundaje et. al. after its installation). 
		Please check the "Required packages" section for the details.

-d  OutDir 		 	 
		Output directory (absolute path preferred) which will store the IDR results.

-n 	PREFIX 			 
		Prefix of output files. Default 'IDR_ATAC'.

-c  CountPeak		 
		No of peaks in both replicates that will be compared for IDR analysis.
		Default 25000.
	
-C  CONTROLBAM		 
		Control file (in eiher .BAM or tagalign file in .gz format)	
		used to estimate the peaks from MACS2. User may leave this field 
		blank if no control file is available.

A sample execution of this script is as follows:

./IDR_SubSampleBAM_Main.sh -I inpfile1.bam -I inpfile2.bam -P /home/sourya/packages/idrCode/ -d /home/sourya/OutDir_IDR -n 'IDR_test' -c 25000 -C control.bam

F1: Folders of the name $i$_and_$j$ where 0 <= i < N and 1 <= j <= N, where N is 
the number of replicates analyzed. Individual folders contain results for 
pairwise IDR analysis. For example, folder 0_and_1 contain IDR analysis 
for the sample 0 (first replicate) and the sample 1 (second replicate).

f1 : "Replicate_Names.txt" : names of the replicate samples used for IDR analysis.

f2: Input_Peak_Statistics.txt: number of peaks and the peak containing replicates.

f3: IDR_Batch_Plot-plot.pdf: final IDR plot. Here individual pairs (whose results 
	are stored in the above mentioned folders) are numbered 1, 2, ...
	Consideing N = 3, the number of pairs possible is also 3. Here, 
	the number 1 denotes the folder (pair) 0_and_1, 
	2 denotes the folder (pair) 0_and_2, and 3 denotes the 
	folder (pair) 1_and_2.